[gmx-users] Problem in rmsf calculation

[Sarath Chandra]

If you have selected C-alpha atoms on x-axis rmsf tool will write C-alpha
atom index number so that is why you do not see 1-143.

Run a gawk on your RMSF output to set the column 1 right.




On 16 June 2016 at 10:48, Seera Suryanarayana <palusoori at gmail.com> wrote:

> Dear gromacs users,
>
> After mdrun I have plotted the rmsf for C-alpha atoms. My protein has 143
> C-alpha atoms and I expected only that number in the plot. But I got rmsf
> values for all atoms of the protein(more than 2250 atoms).  I have attached
> the plot for more information. What could be the reason?
>
> Surya
> Graduate student
> India.
>
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